File Transfer

A number of options exist for transfering files to-and-fro between JHPCE and your local host. Which solution you chose, depends on your use case.

  1. scp or sftp — file transfer via command line
  2. GUI for sftp — file transfer by drag and drop from your desktop
  3. GlobusOnline — fast file transfers between GlobusOnline endpoints
  4. Aspera  —  very fast file transfer to and from Aspera servers
  5. OneDrive access with rclone  —  Use “rclone” to access your OneDrive directory (as well as other network drives (AWS buckets, Google Drive…)
  6. Aspera  —  very fast file transfer to and from Aspera servers
  7. Unison — keep directories synced between the cluster and your local computer
  8. Mount remote filesystems — directories at JHPCE mounted on your local host.
  9. ftp (kind of…)

For transferring files, you should use “jhpce-transfer01.jhsph.edu” rather than “jhpce01.jhsph.edu” when connecting. The “jhpce01.jhsph.edu” node is only meant to be used for logging into the cluster, and not transferring large files. The “jhpce01.jhsph.edu” node only has a 1 Gb/s network connection to the JHU network, whereas the “jhpce-transfer01.jhsph.edu” node has a 40 Gb/s connection. While an individual file transfers would not be able to achieve the full 40Gb/s speed, it will be significantly faster than using the 1Gb/s connection on the “jhpce01.jhsph.edu

scp or sftp

The scp and sftp command-line tools are the most common tools used for transferring data to and from the cluster.  The basic tradeoff is between speed (scp is faster) and flexibility (sftp is more flexible). The differences are described below (taken from wikipedia ).  The scp and sftp commands are available from the Terminal on a MacOS or Linux based laptop/desktop, or from a CMD or Powershell prompt on recent Windows 10 systems.

The “scp” command can be though of as a “network cp” command.  The command to transfer a file called “data.txt” from your local system to your home directory on the cluster would be:

scp data.txt USERID@jhpce-transfer01.jhsph.edu:~

The tilde “~” is a shortcut to represent your home directory.   Once you enter the above comand, you will be prompted for you password on the JHPCE cluster, and when that is entered correctly, your data transfer will begin.

You can also specify a different target directory other than your home directory.  For example, if you want to copy the “data.txt” file to /dcs04/mylab/data on the cluster you would run:

scp data.txt USERID@jhpce-transfer01.jhsph.edu:/dcs04/mylab/data

If you want to copy a file from the cluster to your local laptop/desktop, you would reverse the arguments.  For example, if you ant to copy the file data2.txt from your home directory on the cluster, you would run:

scp USERID@jhpce-transfer01.jhsph.edu:~/data2.txt   .

Note that there is a space and a period at the end of that command.  The period stands for your current directory.

The “sftp” command is another means of transfering data to and from the cluster.  To use sftp, you would run the command:

sftp USERID@jhpce-transfer01.jhsph.edu

As with scp, you would be prompted for your password.  Once you’ve connected, you’ll be shown an “sftp>” prompt.  From here you can use the shell command “ls” to get a directory listing, and and “cd” to change directories.  In addition to “ls” and “cd” you can use the “get” command to transfer a file from the cluster it to your local system, or the “put” command to transfer a file from your local system to the cluster.  Once you are done with sftp, you would type “exit” to end the session.

Although both SCP and SFTP utilize the same SSH encryption during file transfer with the same general level of overhead, SCP is usually faster than SFTP at transferring files, especially on high latency networks.  SFTP should be used when you may need an interactive session on the cluster to navigate to a directory before transferring the files, whereas SCP should be used when you know the exact path of the file you want to transfer.

Graphical User Interfaces for drag and drop file transfer

If you prefer drag and drop interface rather than using shell commands, then an application that presents a window for drag and drop is what you want. Depending on which OS you are using, we can recommend the following applications:

  • Apple OSX Filezilla is an outstanding application that not only provides a GUI browser for FTP, SFTP, but it also allows you to browse WebDav, Amazon S3, and OpenStack Swift file systems. It is free to download and install.  We have information on setting up Filezilla for the JHPCE cluster at the bottom of our 2 Factor Authentication page.
  • Microsoft Windows MobaXterm is our recommended application for accessing the JHPCE cluster, or transferring files to and from the cluster.  Instructions for setting up MobaXterm for file transfer can be found here.  You can also use WinSCP  if you are already familiar with it.

Rclone

Rclone can be used to access network file resources, such as OneDrive, Google Drive, and AWS. See here for an example of connecting to OneDrive.

Aspera

Aspera is a commercial product that allows file transfers that are reportedly 20 times faster than ftp. If you download data from the NCBI Aspera server or download/upload data from/to JHU CIDR on the Bayview campus, then you will use Aspera. The Aspera license does not allow us to install the client for our users. You must install it yourself. You may either download the linux client from the aspera site  or else use the client that we already downloaded. If you prefer the latter, simply copy the installation script from here:

/jhpce/shared/jhpce/core/JHPCE_tools/1.0/packages/aspera-connect-3.6.2.117442-linux-64.sh

into your home directory, and then run the script:

bash aspera-connect-3.6.2.117442-linux-64.sh

This will install the “ascp” command under your home directory at  ~/.aspera/connect/bin .  You can either add ” ~/.aspera/connect/bin” to your PATH, or use the full path to the “ascp” command to run it.

Unison

Using Unison, you can keep data synchronized between a directory on the cluster and a directory on your local system.  Please see this excellent document written by Jacob Fiksel, one of our expert JHPCE cluster users:  https://github.com/jfiksel/cluster-example#how-to-use-unison-for-file-transfer-and-syncing

Globus

See:  http://jhpce.jhu.edu/knowledge-base/using-globus-to-transfer-files/

Mounting virtual file systems

A common use case occurs when a user has a pipeline that is periodicially emiting tab delimited files and the user wants to plot these files with a favorite plotting or analysis application that runs on their local host. In this case it is common to mount the remote file system on the local host via NSF or SMB.

Unfortunately, given the size and hetergeneity of our user base (which spans the entire medical campus), this is not practical. Instead, we recommend that users create a virtual file system on their OSX machine with the MACFusion application. MacFusion is free and allows you to create a mount point on your local host that looks like just another directory in your local file system. So any applications and scripts on your local host can access the data in that mount point. From the user perspective, it acts just like an SMB or NSF mount point. Data is transferred back and forth via an encrypted link.

MacFusion requires the installation of an OSX kernel extenstion and some associated tools. OSXFuse provides the needed extension. OSXFuse implements a so called ” FileSystem in USErspace”. This technology is described here. There exist FUSE kernel modules for most flavors of unix and linux.  The procedure for installing OSXFuse and MACFusion is described below.

  1. Downloaded OSXFUSE from sourceforge repository
    http://sourceforge.net/projects/osxfuse/
  2. install OSXFUSE
    Launch the OSXFUSE installer and perform a custom install.  Be sure to select “MacFuse Compatibility Layer” in the Custom Install screen. After installing the kernel extension it may, or may not, be necessary to reboot your mac.Screen Shot 2014-02-13 at 1.25.09 PM
  3. Download and install the Macfusion app from:
    http://macfusionapp.org
  4.   Startup MacFusion, and create an entry for enigma2.jhsph.edu
    — enter your login and password.
    — select a mount point, e.g. ~/jhpce/myhome/
  5. Once the drive is mounted, you can cd to the directory in the shell or view it  in a window on your desktop. To do this you need to “Reveal” the drive by pressing ⌘-R.  Once the directory is revealed, you can drag and drop files into the director in the usual way you drag and drop files into any directory on your mac.

ftp

We don’t have the ftp client installed on the cluster.  It is an older, less secure, unencrypted channel for transferring files.  However if you are downloading files from an older site that does not support SFTP or one of the other more modern mechanisms, you have a couple of options for ftp.

If you want to be able to interactively browse through the ftp site you can use the “lynx” text based browser command:

lynx ftp://USER@ftp.site.gov

Once connected, you can then use the arrow keys to move around the site, and to select a file to download or a directory to descend into.

If you know the exact path to the file you want, you can use the “wget” command:

wget ftp://USER:PASSWORD@ftp.site.gov/path/to/file

All of these should be done from the “rnet” queue to make use of our high speed ScienceDMZ network connection.